Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 0.129933211900425 0.168184578020644 0.000610526140154569 0.00108986398338977 0.150717703349282
biological_process el 0.0103155339805825 0.0242718446601942 0.000470839005909212 0.00207790951652707 0.0179900744416873
biological_process ka 0.13357619914997 0.171220400728597 0.000453997019585433 0.000792565544613928 0.173853989813243
biological_process rf 0.00364077669902913 0.0121359223300971 0.0032327164803559 0.00915573299934875 0.00236406619385343
cellular_component ct 0.0679459951456311 0.0964805825242718 0.000410515254668196 0.000876423173383597 0.099361249112846
cellular_component el 0.000606428138265616 0.00667070952092177 0.00112426457832003 0.00664783948961097 0.00287769784172662
cellular_component ka 0.0703731796116505 0.098316140776699 0.000449080427074444 0.00113529563766816 0.0987569060773481
cellular_component rf 0.00303214069132808 0.0109157064887811 0.00328628579555785 0.0112871370691079 0.00222613857712643
disease ct 0.275342465753425 0.342482876712329 0.000640083721977323 0.000916941227293608 0.309914642153644
disease el 0.0574948665297741 0.0910506502395619 0.00126664553334461 0.00255318721730125 0.0562560620756547
disease ka 0.291078767123288 0.358236301369863 0.000418594675501282 0.000645559723401084 0.3674228337672
disease rf 0.00684462696783025 0.0184804928131417 0.00836853694538719 0.0199558238527466 0.00234350909651557
gene_PS el 0.328793774319066 0.417315175097276 0.00129831492092424 0.0017672005543494 0.28044537230341
gene_PS ka 0.374489299610895 0.441658560311284 0.000945232576312484 0.00136233625132515 0.331782945736434
gene_PS rf 0.316147859922179 0.401750972762646 0.00108739758940861 0.00158739947238892 0.294162244124337
gene_TF el 0.00714285714285714 0.0642857142857143 0.0108323768923867 0.07456113023993 0.00562429696287964
gene_TF ka 0.0428571428571429 0.135714285714286 0.0445972017270591 1 0.00450704225352113
gene_TF rf 0 0.0428571428571429 0.00294009946985845 0.0610203858556047 0.00710059171597633
gene_hgncGroup el 0.0810611643330877 0.116433308769344 0.00060002450289424 0.00146197308897185 0.105263157894737
gene_hgncGroup ka 0.111274871039057 0.148857774502579 0.00041101629047259 0.000921509720798742 0.155866900175131
gene_hgncGroup rf 0.0913780397936625 0.1319270449521 0.000501255443989809 0.00101504227407936 0.12683313515656
genetic_interaction_effect_bicor ct 0.0311332503113325 0.0510585305105853 0.000476413172818198 0.00130950977134097 0.0473330978452844
genetic_interaction_effect_bicor el 0.0012453300124533 0.0087173100871731 0.000534891137720699 0.00228728707267133 0.00635144671841919
genetic_interaction_effect_bicor ka 0.0336239103362391 0.0516967621419676 0.000425586655660731 0.00102916662199972 0.0520361990950226
genetic_interaction_effect_bicor rf 0.00062266500622665 0.0049813200498132 0.00114971377421397 0.00631257839048916 0.0018984337921215
molecular_function ct 0.0667483159828536 0.093692590324556 0.000468532512745182 0.00121478915970971 0.0877887788778878
molecular_function el 0.000611995104039168 0.00611995104039168 0.00129952907966073 0.00750156313894129 0.00234100663285213
molecular_function ka 0.0642988364972443 0.0918707899571341 0.000616272149073514 0.00133602799877165 0.0818494220556076
molecular_function rf 0.570991432068543 0.61750305997552 0.552912978670079 0.598954939387144 0.00178251156062467
pathway el 0.179447852760736 0.248504601226994 0.000504021062954794 0.00108155231653206 0.239600665557404
pathway ka 0.193251533742331 0.271472392638037 0.000674747519618379 0.00166092025703366 0.250587314017228
pathway rf 0.174846625766871 0.243865030674847 0.000577488539927865 0.00138405038160374 0.233360723089564
phenotype ct 0.262998647734956 0.32657200811359 0.000624453974471132 0.000923017314027199 0.296368989205103
phenotype el 0.154158215010142 0.203515889114266 0.000588711418408546 0.00104019164195117 0.184677149548344
phenotype ka 0.225152129817444 0.290736984448952 0.000406192442441698 0.000595342524899359 0.308575803981623
phenotype rf 0.0189189189189189 0.0351351351351351 0.0166236586125933 0.0301827480511077 0.00222890894906943
protein_interaction el 0.263379434756464 0.317498496692724 0.00159482896820349 0.00218543501846686 0.180760138206947
protein_interaction ka 0.260974143114853 0.309696331930247 0.000635557941268034 0.000962412617247253 0.272212790039615
protein_interaction rf 0.271033653846154 0.330528846153846 0.000719786547574045 0.000999840722581659 0.281377066955815

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 0.330137807070102 0.384661473936489 0.000623857268862939 0.000883082050345744 0.335810624827966
integration_mean_by_presence el 0.00119331742243437 0.00715990453460621 0.000259008223427741 0.00709247560465173 0.00314253647586981
integration_mean_by_presence ka 0.340880597014925 0.404194029850746 0.000332871176110626 0.000521670865064966 0.41851368970013
integration_mean_by_presence rf 0.0835820895522388 0.112238805970149 0.000507270128075513 0.000936150491933279 0.10651267244145
mean ct 0.386458957459557 0.449985020970641 0.000474681835364427 0.000703060912230534 0.423473901503981
mean el 0.0967164179104478 0.154029850746269 0.000493946561083489 0.000760712840328014 0.160628844839371
mean ka 0.367746268656716 0.436417910447761 0.000480110055997452 0.000713535359131042 0.415700267618198
mean rf 0.196417910447761 0.266283582089552 0.000494972437271518 0.000750466901900077 0.267954911433172

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels